Origin of the diversity in DNA recognition domains in phasevarion associated modA genes of pathogenic Neisseria and Haemophilus influenzae

• Published in: PloS one 2012-03, Vol.7 (3), p.e32337-e32337
• Main Authors: Gawthorne, Jayde A, Beatson, Scott A, Srikhanta, Yogitha N, Fox, Kate L, Jennings, Michael P
• Format: Article
• Language: English
• Subjects: Alleles; Amino Acid Sequence; Amino acids; Analysis; Bacteria; Bioinformatics; Biology; Deoxyribonucleic acid; DNA; DNA methylation; DNA methyltransferase; DNA, Bacterial - genetics; Enzymes; Epigenetics; Gene expression; Gene sequencing; Gene transfer; Genes; Genes, Bacterial; Genomes; Haemophilus; Haemophilus influenzae; Haemophilus influenzae - genetics; Helicobacter pylori; Hemophilus infections; Infectious diseases; Medicine; Methylation; Molecular Sequence Data; Mosaicism; Neisseria; Neisseria - genetics; Neisseria gonorrhoeae; Neisseria meningitidis; Nucleotide sequence; Phylogeny; Recognition; Recombination; Recombination, Genetic; Relational data bases; Restriction-modification; Sequence Homology, Amino Acid; Species Specificity; Transferases; Variability
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0032337

Phase variable restriction-modification (R-M) systems have been identified in a range of pathogenic bacteria. In some it has been demonstrated that the random switching of the mod (DNA methyltransferase) gene mediates the coordinated expression of multiple genes and constitutes a phasevarion (phase variable regulon). ModA of Neisseria and Haemophilus influenzae contain a highly variable, DNA recognition domain (DRD) that defines the target sequence that is modified by methylation and is used to define modA alleles. 18 distinct modA alleles have been identified in H. influenzae and the pathogenic Neisseria. To determine the origin of DRD variability, the 18 modA DRDs were used to search the available databases for similar sequences. Significant matches were identified between several modA alleles and mod gene from distinct bacterial species, indicating one source of the DRD variability was via horizontal gene transfer. Comparison of DRD sequences revealed significant mosaicism, indicating exchange between the Neisseria and H. influenzae modA alleles. Regions of high inter- and intra-allele similarity indicate that some modA alleles had undergone recombination more frequently than others, generating further diversity. Furthermore, the DRD from some modA alleles, such as modA12, have been transferred en bloc to replace the DRD from different modA alleles.